Spatiotemporal variation in urban wastewater pollution impacts on river microbiomes and associated hazards in the Akaki catchment, Addis Ababa, Ethiopia

Hiruy, Andualem Mekonnen; Mohammed, Jemila; Haileselassie, Mihret Mersha; Acharya, Kishor; Butte, Giacomo; Haile, Alemseged Tamiru; Walsh, Claire; Werner, David

doi:10.1016/j.scitotenv.2022.153912

Cited by 20 publications

(21 citation statements)

References 40 publications

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“…Min-ION applications comprised a wide range of sample types (Figure 3b), addressed a plethora of water research topics (Figure 3c), and included case studies from high, low, and upper middle-incomes, and least developed countries (Figure 3d). MinION applications were uneven in geographic distribution, and studies in the least developed countries were all from our own work [27,50,54,66,71]. However, the diversity of samples analyzed, the variety of remits, and notable applications in countries without universal access to safe water and sanitation support the utility of the MinION platform for water researchers.…”

Section: Trends In Minion Applications In Water Researchmentioning

confidence: 92%

“…Truelove et al [73] used the MinION onboard an oceanographic research vessel but did not detail the equipment available in the ship's wet and dry laboratories. We assembled a suitcase laboratory for the taxonomic classification of bacteria in water samples by 16S rRNA gene amplicon sequencing and used it at a sewage treatment plant in the UK and for fieldwork in low-resource settings in Africa and South Asia [27,66,71]. This suitcase laboratory contained a small thermocycler from miniPCR bio (Cambridge, MA, USA) that was famously used in combination with the MinION for sequencing DNA in the international space station [81].…”

Section: Portability Of Sample Preparation Methodsmentioning

confidence: 99%

“…Zooplanktonic biomass can be harvested with meshes having 200 µm openings [36], while the biomass of algae [74] and cyanobacteria [48] can be isolated by medium to large volume centrifugation (0.05 to 1 L). Most studies targeting bacteria and archaea filtered between 0.1 and 4 L of water through membranes with 0.22 µm pore size to capture the biomass [27,37,47,50,54,59,63,66,[68][69][70][71]73]. Filtration can take hours to complete [27], and sometimes water prefiltration through membranes with a pore size between 0.4 and 11 µm was used to remove suspended solids [37,76].…”

Section: Biomass Collection and Concentrationmentioning

confidence: 99%

“…Amplification of specific genes or genome regions of interest, targeted with appropriate primers, additionally assures that the full capacity of the MinION is devoted to sequencing these genes or regions. Several studies used full-length 16S rRNA gene amplicon sequencing to characterize communities of bacteria and archaea [27,29,38,48,50,54,56,63,65,66,68,71], mostly with ONT's 16S barcoding kit. Long-range PCR amplicons spanning 3 kb of the rDNA cassette were used for the detection of algal bloom organisms [74].…”

Section: Amplification Of Genes Of Interestmentioning

confidence: 99%

“…Several 16S rRNA gene amplicon studies used ONT's FASTQ 16S workflow to classify bacteria in drinking water [54], groundwater [50], river water [27,63,65,66,68,71], wastewater [38,66,71], aquaculture ponds [68], and sea lice [29]. Van der Loos et al [59] used EPI2ME and Kraken2 with three different reference databases (SILVA [98], Greengenes [99] and NCBI) and recommended assigning taxonomy of nanopore-derived long-reads with Kraken2 and the SILVA database in seaweed-microbiome studies to avoid misidentifications of cyanobacteria due to chloroplast contamination.…”

Section: Taxonomic Classificationmentioning

confidence: 99%

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MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

Werner

Acharya

Blackburn

et al. 2022

Water

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In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications.

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Section: Trends In Minion Applications In Water Researchmentioning

confidence: 92%

Section: Portability Of Sample Preparation Methodsmentioning

confidence: 99%

Section: Biomass Collection and Concentrationmentioning

confidence: 99%

Section: Amplification Of Genes Of Interestmentioning

confidence: 99%

Section: Taxonomic Classificationmentioning

confidence: 99%

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MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

Werner

Acharya

Blackburn

et al. 2022

Water

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Cold atmospheric plasma can effectively disinfect SARS‐CoV‐2 in the wastewater

Qin,

Qiu,

Liu

et al. 2023

Exploration

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COVID‐19 is currently pandemic and the detection of SARS‐CoV‐2 variants in wastewater is causing widespread concern. Herein, cold atmospheric plasma (CAP) is proposed as a novel wastewater disinfection technology that effectively inactivates SARS‐CoV‐2 transcription‐ and replication‐competent virus‐like particles, coronavirus GX_P2V, pseudotyped SARS‐CoV‐2 variants, and porcine epidemic diarrhoea virus in a large volume of water within 180 s (inhibition rate > 99%). Further, CAP disinfection did not adversely affect the viability of various human cell lines. It is identified that CAP produced peroxynitrite (ONOO−), ozone (O3), superoxide anion radicals (O2−), and hydrogen peroxide (H2O2) as the major active substances for coronavirus disinfection. Investigation of the mechanism showed that active substances not only reacted with the coronavirus spike protein and affected its infectivity, but also destroyed the nucleocapsid protein and genome, thus affecting virus replication. This method provides an efficient and environmentally friendly strategy for the elimination of SARS‐CoV‐2 and other coronaviruses from wastewater.

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Anthropogenic land uses drive shifts in denitrification‐related microbiota in freshwater river ecosystems

et al. 2022

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Microbiota play essential roles in nitrogen (N) cycling in freshwater river ecosystems. However, our understanding of microbial functional groups associated with N cycling (especially denitrification) in freshwater rivers under anthropogenic disturbance is still poor. Here, we studied the impacts of different land-use types on denitrificationrelated microbiota in the Weihe River, Hanjiang River, and their tributaries, in the Qinling Mountains, China. The major land-use types in the three river areas were divided into natural (forest, shrub, grassland, and open water) and anthropogenic (agricultural and urbanized land) types. A landscape survey of microbiota in the river water and sediment was carried out with extensive sample sources based on deep 16S rRNA gene sequencing, which yielded operational taxonomic units for predicting functional groups. With increases in proportions of agricultural and urbanized land areas, electrical conductivity, total N, ammonium-N, and nitrate-N all increased in water samples. Conversely, microbial diversity exhibited a decreasing trend in water samples, whereas the relative abundance of denitrification-related functional groups increased, with increases in the proportions of agricultural and urbanized land areas.The relative abundances of denitrification-and human-related microbial functional groups in sediment samples were distinctively higher in Weihe River (mainly under agriculture and urbanization), when compared with those of Hanjiang River and Qinling tributaries (dominated by forests). The results indicate that anthropogenic landuse types, such as agricultural and urbanized land, result in simple microbial community structure and stimulate microbe-mediated denitrification in freshwater rivers.agricultural land, denitrification, freshwater ecosystems, land-use type, microbiota, urbanized land | BACKGROUNDFreshwater is a fundamental component of aquatic ecosystems and is important for coupling of biogeochemical cycles in lands, rivers, and oceans (Aufdenkampe et al., 2011). The emission of greenhouse gases (GHG) from freshwater ecosystems is source of concern globally (Liu

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Spatiotemporal variation in urban wastewater pollution impacts on river microbiomes and associated hazards in the Akaki catchment, Addis Ababa, Ethiopia

Cited by 20 publications

References 40 publications

MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

Cold atmospheric plasma can effectively disinfect SARS‐CoV‐2 in the wastewater

Anthropogenic land uses drive shifts in denitrification‐related microbiota in freshwater river ecosystems

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